According to the man page, command line options for xboard can be placed in ~/.Xresources.

This manual documents version master-20110822 of XBoard.

OPTIONS This section documents the command-line options to XBoard. You can set these options in two ways: by typing them on the shell command line you use to start XBoard, or by setting them as X resources (typically in your `.Xresources' file). Many of the options cannot be changed while XBoard is running; others set the initial state of items that can be changed with the Options menu.

Most of the options have both a long name and a short name. To turn a boolean option on or off from the command line, either give its long name followed by the value true or false (`-longOptionName true'), or give just the short name to turn the option on (`-opt'), or the short name preceded by `x' to turn the option off (`-xopt'). For options that take strings or numbers as values, you can use the long or short option names interchangeably.

Each option corresponds to an X resource with the same name, so if you like, you can set options in your `.Xresources' file or in a file named `XBoard' in your home directory. For options that have two names, the longer one is the name of the corresponding X resource; the short name is not recognized. To turn a boolean option on or off as an X resource, give its long name followed by the value true or false (`XBoard*longOptionName: true').

I see that this is no longer the case, and that /usr/local/etc/xboard.conf and ~/.xboardrc now store preferences.

Updating docs is a pain, as there are currently three sets of docs that have to be maintained independently (one for XBoard, and two for WinBoard), some in an extremely cumbersome way (for the WinBoard HTML docs I have to maintain the index and contents by hand).

Arun was looking for a method to unify the XBoard and WinBoard HTML docs (we would then abandon the old WinBoard HLP format), which should be possible now XBoard and WinBoard have almost entirely converged. But it seems this effort has stalled. And I am really not very motivated to put a huge effort in maintaining docs that will be scrapped soon...

After not using Xboard for several years, I decided to try it again. (Lots of nice improvements. Thanks.) When the program didn't use the Xboard options from my ~/.Xresources file as it did previously, I went to the man page!